Background: Memory and in turn, memory of pain is a reconstructive process. This study considers the relationship between time, memory, affective states, and pain induced by running a marathon by investigating the influence of these factors on a participant's memory of pain experienced after a marathon. The following two hypotheses were formulated: 1) participants' recalled-pain of marathon experience is underestimated; and 2) the underestimation of recalled pain would be greater for participants experiencing higher positive affect. Methods: A longitudinal design was employed to check pain intensities of marathon participants a) at the finish line and b) 6 months following its completion. The sample size was based on a power analysis, and 108 marathonists rated their pain intensities and positive and negative affects at the finish line. From this sample, 58 participants recalled their pain experience of running the marathon 6 months later. Linear models, including computer-based data-mining algorithms, were used. Results: The experienced pain was higher than their recalled pain (t(55) = 3.412, p < 0.01, d = 0.45), supporting the first hypothesis. The memory of pain faded similarly in all participants, which did not directly support the second hypothesis. Further exploratory analysis suggested that negative and positive affective states were related to participants' pain memory; positive affective states appeared to be inversely related to the recall (β = −0.289, p = 0.039). Discussion: This study shows that time has a significant effect on memory recall and that emotions may also influence the memory of pain. This is the first study that preliminarily showcased the effect of positive affective states on the memory of pain induced by physical exercise.